From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Aug 29 2006 - 17:00:51 CDT
Dear NAMD users,
I was wondering if there is a quick way to count the number of
hydrogen bonds between a lipid molecule and a protein chain directly
from the dcd file. I also want to use different paprameters for
H-bonds (60 degrees as angle and 3.5 Ang as the distance cut-off).
thanks a lot in advance.
Rgds,
Nitin
On 03/08/06, Jerome Henin <jhenin_at_vitae.cmm.upenn.edu> wrote:
> Sukesh,
>
> You can very easily generate a waterbox and the associated topology (PSF
> format) with the Solvate plugin of VMD. In VMD use the menu item
> Extensions->Modeling->Add solvation box, and specify no input files, but check
> the "waterbox only" box.
> See a description there:
> http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
>
> Jerome
>
>
> On Thursday 03 August 2006 14:19, Shenoy, Sukesh wrote:
> > I want to generate the psf file for simulating a 1000 water molecules. The
> > problem is that NAMD requires that the psf contain the bonds, angles and
> > dihedral information for all the 1000 water molecules. It is cumbersome and
> > time consuming to do this manually. Does anybody know how one can do this
> > quickly (through a program perhaps)?
> >
> > Sukesh
>
-- $B&-(BI+I$B'*(B
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